Histone deacetylases (HDACs) and histone acetyltransferases (HATs) are two functionally opposing enzymes which tightly regulate chromatin structure and function by maintaining the equilibrium between the acetylated- and deacetylated-states of nucleosomal histones. Aberrations in intracellular histone acetylation-deacetylation equilibrium have been linked to the repression of a subset of genes resulting in excessive proliferation and are implicated in a number of malignant diseases (Jenuwein, T.; Allis, C. D., Science 293, 1074-1080 (2001); Marks, P.; Rifkind, R. A.; Richon, V. M.; Breslow, R.; Miller, T.; Kelly, W. K., Nat. Rev. Cancer, 1, 194-202 (2001)). HDACs function as part of multiprotein complexes that catalyze the removal of acetyl groups from the ε-amino groups of specific lysine residues located near the N-termini of nucleosomal core histones (Grozinger, C. M.; Schreiber, S. L., Chem. Biol. 9, 3-16 (2002)). HDAC-catalyzed deacetylation results in positively charged, hypoacetylated histones which bind tightly to the phosphate backbone of DNA, thus inducing gene-specific repression of transcription. Inhibition of HDAC function results in the weakening of the bond between histones and DNA, thus increasing DNA accessibility and gene transcription.
Eighteen distinct human HDACs have been identified to date. They are classified into three major families based on their homology to three Saccharomyces cerevisiae HDACs: RPD3, HDA1, and SIR2. Class I includes HDACs 1, 2, 3 and 8. Class II includes HDACs 4, 5, 6, 7, 9, 10 and 11. The third class of HDACs is the sirtuins, which are homologically distinct from all the currently known HDACs. HDAC inhibition by small molecules has been observed for the natural product (R)-trichostatin A which induced cell differentiation of murine erythroleukemia cells and hyperacetylation of histone proteins at nanomolar concentrations. Suberoylanilide hydroxamic acid (SAHA) has also been identified as a HDAC inhibitor.
Inhibition of HDACs is an emerging therapeutic strategy in cancer therapy. HDAC inhibitors have demonstrated ability to arrest proliferation of nearly all transformed cell types, including epithelial (melanoma, lung, breast, pancreas, ovary, prostate, colon and bladder) and hematological (lymphoma, leukemia and multiple myeloma) tumors (Kelly, W. K; O'Connor, O. A.; Marks, P. A., Expert. Opin. Investig. Drugs, 11, 1695-1713 (2002)). Additionally, HDAC inhibitors have demonstrated other biological activity including anti-inflammatory, anti-arthritic, anti-infective, anti-malarial, cytoprotective, neuroprotective, chemopreventive and/or cognitive enhancing effects.
All HDAC inhibitors so far reported typically fit a three-motif pharmacophoric model namely, a zinc-binding group (ZBG), a hydrophobic linker and a recognition cap-group (Miller, T. A.; Witter, D. J.; Belvedere, S., J. Med Chem., 46, 5097-5116 (2003)). Structural modifications of the ZBG yielding hydroxamate isosteres such as benzamide, α-ketoesters, electrophilic ketones, mercaptoamide and phosphonates have been reported. The cap-group may present opportunities to discover more potent and/or selective HDAC inhibitors. Toward this end, recent work by Schreiber and co-workers has led to the identification of cap group-modified agents that display differential inhibition against specific HDAC sub-types (Wong, J.; Hong, R.; Schreiber, S., J. Am. Chem. Soc. 125, 5586-5587 (2003); Haggarty, S. J.; Koeller, K. M.; Wong, J. C.; Grozinger, C. M.; Schreiber, S. L., Proc. Natl. Acad. Sci. USA, 100, 4389-4394 (2003)).
Cyclic-peptide moieties are the most complex of all HDAC inhibitor cap-groups and present an opportunity for the modulation of the biological activities of HDAC inhibitors. The macrocycle group is made up of hydrophobic amino acids and the prominent difference among the members of this class is in the amino acid side-chain substitution on the ring. Mechanistically, cyclic-peptide HDAC inhibitors can be divided into two classes: (i) reversible HDAC inhibitors and (ii) irreversible HDAC inhibitors, due to the alkylative modification of HDAC enzyme by the epoxy-ketone moiety on their side-chain. HDAC inhibitory activity and selectivity can vary significantly by changing the side-chain of each amino acid and/or the pattern of the combination of amino acid chirality.
Although cyclic-peptide HDAC inhibitors may possess potent HDAC inhibitory activity, their broad application in specific therapies, such as cancer therapy, currently remains largely unproven. The absence of clinically effective cyclic-peptide HDAC inhibitors may be in part due to development problems characteristic of large peptides, particularly poor oral bioavailability. In fact, the overall in vivo efficacy of cyclic-peptide HDAC inhibitors is complicated by their membrane penetration ability. HDAC inhibitory potency has been noted to increase with increase in the hydrophobicity of the macrocyclic ring (Meinke, P. T.; Liberator, P., Curr. Med. Chem., 8, 211-235 (2001)). Unfortunately, SAR studies for this class of compounds have been impaired largely because most macrocyclic HDAC inhibitors known to date contain peptide macrocycles. In addition to retaining the pharmacologically disadvantaged peptidyl-backbone, they offer only limited opportunity for side-chain modifications.
To date, several other structurally distinct small molecule HDAC inhibitors have been reported including hydroxamates, benzamides, short-chain fatty acids, electrophilic ketones and cyclic-peptides (Miller, T. A.; Witter, D. J.; Belvedere, S., J. Med. Chem. 46, 5097-5116 (2003); Rosato, R. R.; Grant, S., Expert Opin. Invest. Drugs, 13, 21-38 (2004); Monneret, C., Eur. J. of Med. Chem., 40, 1-13 (2005); Yoo, C. B.; Jones, P. A., Nature Reviews Drug Discovery, 5, 37-50 (2006)). Most of these agents have been shown to non-selectively inhibit the deacetylase activity of class I/II HDAC enzymes. The HDAC inhibitor SAHA has been approved by the FDA for the treatment of cutaneous T cell lymphoma. However, a large number of the identified HDAC inhibitors have elicited only limited in vivo antitumor activities and have not progressed beyond preclinical characterizations.
Therefore, there is a need to develop new HDAC inhibitors with improved efficacy, and better pharmacokinetic properties for use as therapeutic agents, such as anti-cancer agents and anti-parasitic agents.
It is therefore an object of the invention to provide non-peptide macrocyclic HDAC inhibitors having improved efficacy and methods of making and using thereof.